Are circuits composed of transistors and capacitors patentable?
In principle yes. However, the claimed circuit (like any invention) must fulfil the patentability requirements (primarily novelty and non-obviousness).
If the claim was directed to "a circuit comprising a transistor and a capacitor", it seems very likely that would not be novel. However, if the claim was directed to a particular arrangement of components which, in that particular arrangement produce quite a unique effect, then it may well be novel and non-obvious.
Is there any other protection for manufacturers to protect themselves from clones?
Trade secrets might be relevant: if the function of the device is not really derivable from the final product (for whatever reason), then it might make sense to just keep the construction a secret. In addition, registered designs (which protect appearance) and trade marks (which protect commercial marking) both immediately come to mind as being relevant.
Why are there few patents related to effect pedals?
It is impossible to say conclusively. It may be that there has been very little real innovation in the area, such that there is nothing to patent. Alternatively, there may be characteristics in the industry which make patents less useful: high industrial barriers to entry or high customer loyalty to brands, for example.